الكائنات الدقيقة وأدوارها

Chapter 1: Microorganisms and Their Roles

• Microorganisms, also known as microbes or germs, are tiny organisms invisible to the naked eye.
• Microorganisms are not always associated with diseases; many are crucial for our well-being.
• The human microbiome is a group of microbes living stably on or in the human body.
• The microbiome helps maintain health, prevents growth of harmful microbes, and trains the immune system.
• Normal microbiota are acquired as newborns and colonize the body indefinitely or fleetingly.
• The human microbiome project (2007) aimed to determine the makeup of typical microbiota in various body areas and their relationship to diseases.
• The national microbiome initiative (NMI) (2016) explores the role of microbes in different ecosystems.

Roles of Microorganisms

• Microorganisms can cause diseases and food spoilage.
• They are involved in nitrogen fixation. Soil microbes like Azobacter and Cyanobacteria convert atmospheric nitrogen into usable forms for plants.
• Some microbes use N2 from the air to synthesize N2.
• Photosynthesis is carried out by unicellular algae and cyanobacteria, converting light energy to chemical energy.
  • This contributes to the food chain in waters.
• Microorganisms form the basis of the food chain in oceans, lakes, and rivers.
• During sewage treatment, microbes recycle water by removing solids and excrement.
• Bioremediation is carried out by microbes to clean up pollutants, like oil spills.
• Insect pest control is achieved using Bacillus thuringiensis and B. sphericus, which produce protein crystals toxic to insects.
• Many chemicals are synthesized by microorganisms:
  • Ethyl alcohol through anaerobic fermentation of carbohydrates with yeast.
  • Acetic acid through aerobic oxidation of ethanol using acetobacter.
  • Acetone in glycolysis by removing a phosphate group from glyceraldehyde-3-phosphate.
• Microbes synthesize vitamins like B12, Riboflavin, and C.
• Enzymes such as amylase and streptokinase are made by microorganisms.
• Microbes help in producing:
  • Antibiotics (e.g., Penicillin)
  • Products in the food industry like, vinegar, bread, wine, beer, cheese, yogurt, sour cream
  • Manufactured and treated products (e.g., cellulase, insulin)

Nomenclature and Classification of Microorganisms

• Each organism has two names: genus and specific epithet.
• Scientific names are italicized or underlined with the genus capitalized and the species in lowercase
• Staphylococcus aureus describes clustered cells (staphylo-) with a golden color (aureus) and spherical shape (coccus).
• Escherichia coli honors Theodor Escherich and describes the bacterium's habitat in the large intestine.
• Normal flora competes with pathogens and stimulates the production of vitamins K and B, and antimicrobial peptides.

Classification of Microorganisms

• Early classification included two kingdoms: Animalia and Plantae, with no transitional group.
• Haeckel proposed placing microorganisms in a separate kingdom, Protista.
• Electron microscopy revealed cell structural differences, leading to the classification of prokaryotes and eukaryotes.
• Classification is based on cellular organization into three domains: Bacteria, Archaea, and Eukarya.
• Bacteria and Archaea are only prokaryotes, differing in nucleotide sequences in rRNA.
• Bacteria have peptidoglycan cell walls (not present in archaea).
• Bacteria consumes organic/inorganic chemicals and some are capable of photosynthesis such as Cyanobacteria.

Prokaryotic vs. Eukaryotic Cells

• Prokaryotes are typically small, while eukaryotes are typically large.
• Prokaryotes lack a nuclear membrane or nucleoli, while eukaryotes have a true nucleus with a nuclear membrane.
• Prokaryotes lack complex organelles, while eukaryotes do.
• Prokaryotes may contain peptidoglycan in their cell wall, unlike eukaryotes.
• Prokaryotes have 70S ribosomes, while eukaryotes have 80S ribosomes.
• Prokaryotes have a single circular chromosome, while eukaryotes have multiple linear chromosomes.
• Prokaryotes divide by binary fission, while eukaryotes divide by mitosis.
• Prokaryotes lack histones, while eukaryotes have histones.
• Bacteria, blue-green algae (cyanobacteria), and Archaea are prokaryotes. Algae, fungi, and protozoa are eukaryotes.
• Linnaeus established the scientific nomenclature system with two names for each organism (genus and species).
• Haeckel proposed the kingdom Protista, which included various microorganisms.
• Woese revised the system based on cellular organization, creating three domains of life.

Types of Microorganisms

• Bacteria: Eubacteria in the domain Bacteria, small in size.
• Archaea: Prokaryotic. No peptidoglycan in cell walls. No disease in humans. Found in extreme environments.
• Fungi: Eukaryotes with chitin cell walls.
• Protozoa: Unicellular eukaryotes, absorb/ingest organic chemicals.
• Algae: Eukaryotes with cellulose cell walls
• Viruses: Acellular; contain DNA or RNA surrounded by a protein coat.
• Reproduction: Binary fission

History of Microbiology

• Microbiology dates back about 200 years.
• Hooke used a crude microscope and found "cells", beginning the cell theory.
• Leeuwenhoek made a simple microscope with powerful lenses, observing animal and plant tissues and living animal sperm.
• Spontaneous generation: Life could arise from non-living matter.
• Redi disproved spontaneous generation by showing that maggots arose from decaying meat only when flies laid eggs on it.
• Needham claimed microbes developed spontaneously in heated nutrient fluids.
• Spallanzani nutrient fluids remained sterile when heated after sealing in a flask, contradicting Needham's claim.
• Debate over spontaneous generation: The notion that "vital force" is necessary for spontaneous generation.

Theory of Biogenesis

• Virchow introduced the theory of biogenesis: that living cells arise only from pre-existing cells.
• Pasteur demonstrated that microorganisms are present in the air.
• Pasteur's S-shaped flask was designed to keep microbes out but let air in.
• Beginning with Pasteur's work, the relationship between microbes and disease was discovered.
• It was shown that microbes are responsible for fermentation and spoilage of food.

The Germ Theory of Disease

• Contributed contributions and discoveries

Postulates

Koch's Postulates:

• Koch provided experimental steps in proving that a specific microbe causes a specific disease.
• The same pathogen must be present in every case of the disease.
• The pathogen must be isolated from the diseased host and grown in pure culture.
• The pathogen from the pure culture must cause the disease if inoculated into a healthy animal.
• The pathogen must be isolated from the inoculated animal and is show to become the original organism.

The Birth of Modern Chemotherapy

• Chemotherapy is the treatment with chemicals.
• Chemotherapeutic agents are used to treat infectious diseases. They can be synthetic drugs or antibiotics that are natural.
• Antibiotics are chemicals produced by bacteria and fungi that inhibit or kill other microbes.
• A successful agent involves: destruction of the pathogen only harming the healthy host cell.
• Fleming discovered the first antibiotic, Penicillin.
• Bacteriology is the study of bacteria.
• Mycology is the study of fungi. _ Parasitology is the study of parasites

Normal Microbiota vs Normal Flora

_ The normal microbiota inhibits the growth of pathogens prevents haRmful microbes from overgrowing and overpopulating.

• The human body is not misrobially sterlie _ Each G of feces is made up of ~109 bacteria
• Normal microbiota produces factor growth, such as vitamin B, such as Folic acid + K
• Resistance is when the ability of our body wards off any diseases
• There are 3 factors: skin, antimicrobial chemicals,s and stomach-acids

Biofilms

Biofilms are good with mucous and aquatic animals while harmful and clog water pipes and cause endo-carditis. Bacterial can ppt on the other layer on different surface

Infectious Disease vs. Emerging/Re-Emerging Diseases

• Infectious: Malaria, diphtheria, covid-19 _ Emerging/Re-Emerging: West Nile Virus, bloody diarrhea, Ebola and Cryptosporidiosis and Anthrax
• Emerges: New + the increase of incidence in diseases (EX: covid-19 _ Re-emerging: diseases were once considered health problems then health dramatically improved then again becoming health challenges.

Bacteria Structure and Arrangement

Cocci, Spirillium, bacilli, and stela. Some are chains Note only certain cells have 1 shape, the majority and monophromic while the others are able to have more then to 1 shape. Knowns as pleomorphic

Cyanobacteria

(Blue and Green Aglae) are aerobic phototrophs, the need light and water to survive. Known for using cells to fix nitrogen gas.

Mycoplasma

Microbacteria that lacks cell walls and uses plasma membrane Due to the lack of cell walls not able to be affected when using a cell-antibiotics Note: Small bacteria with primitive features morphology Cell walls have archaea but Lacks peptogiycam

Stuctutes EXTERNAL to wall cell

• Glycocalyex which is made of sugar. Prevents the process to phagocytes
• Capsulated are virulent. Some such as. B. anthracis has D- GLUTAMIC acids AND S. pneumonia -polysaccharide
• It enables the atachement for the cells to survive _ It helps the cells in biofilm attache to another

Fimbiae

Allows the infection to attach it has is used in. Neisseria gonorhoeae, V.colera, + ecol

Pilli

It is used for motility to twitch and glide _ It has conjugations and transfers DNA to the other cell

BACTERIAL PEPTIDOGLYCAN FEATURES

• It contains semi semi rigidness elasticity.
• Rigid mechanical support
• Is permeable to solutes
• In ve- Bacterial it contains meso and diamminopimelix acid
• In ve+ peptidgolycam uses ll-Llysience instead

PENICILLINS and CEPHALOSPORINS

• It is classified as a B lactam antobiotics and Is used to cell walls
• It's selectivity toxic and lysis and weakens the cell walls causing destructions

The Outer Membrane Lipids + GRAM has and the Gram

• Outer membrane has peptidotycan the cell has and B are 2 layers with periplasm. B can live with the cell, + Gram only has the lipo
• Cell walls and membrane are also there
• teichoic acids and wall teochic are in the membrane and cells proteins